'RGUA', 'RCYT', 'RADE', 'RTHY', 'RURA',
)
mapCing2Aqua = {
'GUA': 'G',
'CYT': 'C',
'ADE': 'A',
'THY': 'T',
'URA': 'U',
'RGUA': 'G',
'RCYT': 'C',
'RADE': 'A',
'RTHY': 'T',
'RURA': 'U',
}
for res in NTdb:
res.nameDict[AQUA] = res.nameDict[IUPAC]
if res.name in nuclList:
res.nameDict[AQUA] = mapCing2Aqua[res.name]
for atm in res:
atm.nameDict[AQUA] = atm.nameDict[IUPAC]
stream = open('dbTable-new', 'w')
NTdb.exportDef(stream=stream)
stream.close()
'GUA',
'CYT',
'ADE',
'THY',
'URA',
'RGUA',
'RCYT',
'RADE',
'RTHY',
'RURA',
)
mapCyana2Xplor = {
'OP1': 'O1P',
'OP2': 'O2P',
'H2"': "H2''",
'H5"': "H5''",
}
mapCyana2XplorKeys = mapCyana2Xplor.keys()
for res in NTdb:
if not res.name in nuclList:
continue
for atm in res:
atm.nameDict[XPLOR] = atm.nameDict[CYANA]
if atm.nameDict[CYANA] in mapCyana2XplorKeys:
atm.nameDict[XPLOR] = mapCyana2Xplor[atm.nameDict[CYANA]]
stream = open('dbTable-new', 'w')
NTdb.exportDef(stream=stream)
stream.close()
HIS=['HIS', 'HIS+', 'HIST'],
LYS=['LYS', 'LYS+'],
)
for line in AwkLikeS(shifts):
if (not line.isComment() and line.NF == 8):
if (line.dollar[1] in resEquiv):
resNames = resEquiv[line.dollar[1]]
else:
resNames = line.dollar[1:2]
#end if
for resName in resNames:
res = NTdb[resName]
atm = NTdb.getAtomDefByName(resName, line.dollar[2], IUPAC)
if atm != None:
atm.shift = NTdict(average=line.float(7), sd=line.float(8))
else:
nTmessage('>>> line %d: %s', line.NR, line.dollar[0])
#also get the pseudo shifts
for res in NTdb:
for atm in res:
ave = 0.0
sd = 0.0
n = 0
for aN in atm.real:
a = res[aN]
if a.shift != None:
ave += a.shift.average
if rdef.name != rdef.translate('BMRB'):
printf(' ****\n')
else:
printf('\n')
for adef in rdef:
bname = adef.translate('BMRB')
cname = adef.translate('CYANA2')
if bname != cname:
printf('IUPAC: %-8s CYANA2: %-8s\n', bname, cname)
#end for
print('\n')
#end for
for adef in NTdb.atomsWithProperties('HN'):
adef.aliases = ['HN','H']
for adef in NTdb.atomsWithProperties('C'): # This generated erros with the cys residues
adef.aliases = ['C','CO']
printf('''
===================================================================================
- Changing existing BMRB->IUPAC
- Changing existing INTERNAL->INTERNAL_0
- Adding INTERNAL_1 ResidueDefs:
keep original residue names (manual check required)
- Adding INTERNAL_1 atomDefs:
Use BMRB/IUPAC or CYANA2 if BMRB/IUPAC undefined
Add CYANA2 names as alias if different from BMRB/IUPAC
===================================================================================
HIS = ['HIS', 'HIS+', 'HIST'],
LYS = ['LYS', 'LYS+'],
)
for line in AwkLikeS( shifts ):
if (not line.isComment() and line.NF == 8):
if (line.dollar[1] in resEquiv):
resNames = resEquiv[line.dollar[1]]
else:
resNames = line.dollar[1:2]
#end if
for resName in resNames:
res = NTdb[resName]
atm = NTdb.getAtomDefByName( resName, line.dollar[2], IUPAC )
if atm != None:
atm.shift = NTdict( average=line.float(7), sd=line.float(8) )
else:
nTmessage( '>>> line %d: %s', line.NR, line.dollar[0] )
#also get the pseudo shifts
for res in NTdb:
for atm in res:
ave = 0.0
sd = 0.0
n = 0
for aN in atm.real:
a = res[aN]
if a.shift != None:
ave += a.shift.average
if rdef.name != rdef.translate('BMRB'):
printf(' ****\n')
else:
printf('\n')
for adef in rdef:
bname = adef.translate('BMRB')
cname = adef.translate('CYANA2')
if bname != cname:
printf('IUPAC: %-8s CYANA2: %-8s\n', bname, cname)
#end for
print('\n')
#end for
for adef in NTdb.atomsWithProperties('HN'):
adef.aliases = ['HN', 'H']
for adef in NTdb.atomsWithProperties(
'C'): # This generated erros with the cys residues
adef.aliases = ['C', 'CO']
printf('''
===================================================================================
- Changing existing BMRB->IUPAC
- Changing existing INTERNAL->INTERNAL_0
- Adding INTERNAL_1 ResidueDefs:
keep original residue names (manual check required)
- Adding INTERNAL_1 atomDefs:
Use BMRB/IUPAC or CYANA2 if BMRB/IUPAC undefined
Add CYANA2 names as alias if different from BMRB/IUPAC
===================================================================================
#@PydevCodeAnalysisIgnore # pylint: disable-all
from cing.Libs.NTutils import *
from cing.core.database import ResidueDef
from cing import NTdb
import cing
stream = open('dbTable.new', 'w')
NTdb.exportDef(stream=stream, convention='INTERNAL_1')
stream.close()